+Open data
-Basic information
Entry | Database: PDB / ID: 2y0b | ||||||
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Title | Caspase-3 in Complex with an Inhibitory DARPin-3.4_S76R | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN BINDING / HYDROLASE-PROTEIN BINDING COMPLEX / STRUCTURE-ACTIVITY RELATIONSHIP / ANKYRIN REPEAT PROTEIN / RIBOSOME DISPLAY / APOPTOSIS | ||||||
Function / homology | Function and homology information caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptosis / glial cell apoptotic process / NADE modulates death signalling / response to cobalt ion ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptosis / glial cell apoptotic process / NADE modulates death signalling / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / pyroptosis / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / regulation of macroautophagy / response to amino acid / cell fate commitment / Pyroptosis / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / response to nicotine / apoptotic signaling pathway / hippocampus development / sensory perception of sound / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / response to hypoxia / aspartic-type endopeptidase activity / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Barandun, J. / Schroeder, T. / Mittl, P. / Grutter, M.G. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Specific Inhibition of Caspase-3 by a Competitive Darpin: Molecular Mimicry between Native and Designed Inhibitors. Authors: Schroeder, T. / Barandun, J. / Flutsch, A. / Briand, C. / Mittl, P. / Grutter, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y0b.cif.gz | 303 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y0b.ent.gz | 247.2 KB | Display | PDB format |
PDBx/mmJSON format | 2y0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/2y0b ftp://data.pdbj.org/pub/pdb/validation_reports/y0/2y0b | HTTPS FTP |
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-Related structure data
Related structure data | 2xzdC 2dkoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein , 3 types, 6 molecules ACBDGH
#1: Protein | Mass: 16874.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: T7 PROMOTER EXPRESSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42574, caspase-3 #2: Protein | Mass: 13832.739 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: T7 PROMOTER EXPRESSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42574, caspase-3 #3: Protein | Mass: 14810.638 Da / Num. of mol.: 2 / Fragment: N2C, RESIDUES 1-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Description: T5 PROMOTER EXPRESSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1BLUE |
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-Non-polymers , 3 types, 349 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.3 Details: 100 MM HEPES, PH 7.3 (RT) 40 % 2-METHYL-2,4-PENTANEDIOL |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2010 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49 Å / Num. obs: 62855 / % possible obs: 99.2 % / Observed criterion σ(I): 1.96 / Redundancy: 3.4 % / Biso Wilson estimate: 35.75 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.94 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.96 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DKO Resolution: 2.1→84.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.59 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.484 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→84.87 Å
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Refine LS restraints |
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